PDB-4ru0: The crystal structure of abc transporter permease from pseudomona...

ID or keywords:

Entry

Database: PDB / ID: 4ru0

Title

The crystal structure of abc transporter permease from pseudomonas fluorescens group

Components

Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

Keywords

TRANSPORT PROTEIN / ABC transporter permease / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha/beta fold / solute binding protein / solute / Extracellular

Function / homology

Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / 3,6,9,12,15-PENTAOXAHEPTADECANE / Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

Function and homology information

Biological species

Pseudomonas protegens Pf-5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.442 Å

Authors

Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of abc transporter permease from pseudomonas fluorescens group
Authors: Wu, R. / Endres, M. / Joachimiak, A.

History

Deposition	Nov 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ru0.cif.gz	343.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ru0.ent.gz	280.7 KB	Display	PDB format
PDBx/mmJSON format	4ru0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ru0_validation.pdf.gz	807.9 KB	Display	wwPDB validaton report
Full document	4ru0_full_validation.pdf.gz	816.4 KB	Display
Data in XML	4ru0_validation.xml.gz	37.2 KB	Display
Data in CIF	4ru0_validation.cif.gz	49 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ru/4ru0 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4ru0	HTTPS FTP

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Related structure data

Similar structure data	3qiy-d 1i7o-2 1gtt-1 4e31-d 4f6c-1 2zyk-2 3qj0-d 5v8u-1 3mdw-2 6c1w-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC110875

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

B: Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

hetero molecules

99.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

hetero molecules

defined by author&software
49.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein

hetero molecules

defined by author&software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.181, 99.181, 104.959
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Putative branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid-binding protein Mass: 49152.582 Da / Num. of mol.: 2 / Fragment: residues (27-444) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: Pf-5 / Gene: PFL_2622 / Plasmid: MCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: Q4KDF4
#2: Chemical	ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE Mass: 250.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₅
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.43 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Lithium Sulfate 0.1 M TRIS:HCl pH 8.5 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2012 / Details: MIRRORS
Radiation	Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 2.44→50 Å / Num. obs: 68079 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / B_iso Wilson estimate: 22.23 Å² / R_sym value: 0.044 / Net I/σ(I): 15.6
Reflection shell	Resolution: 2.44→2.48 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4 / Num. unique all: 2111 / R_sym value: 0.345 / % possible all: 97

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.9_1683)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.442→39.748 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 23 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2146	3425	5.03 %
R_work	0.1792	-	-
obs	0.181	68079	79.38 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.442→39.748 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6480	0	54	217	6751

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6695
X-RAY DIFFRACTION	f_angle_d	0.879	9073
X-RAY DIFFRACTION	f_dihedral_angle_d	13.221	2426
X-RAY DIFFRACTION	f_chiral_restr	0.04	954
X-RAY DIFFRACTION	f_plane_restr	0.004	1184

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.4416-2.4764	0.227	73	0.2482	1346	1346	40
2.4764-2.5134	0.3024	75	0.25	1536	1536	45
2.5134-2.5527	0.3234	91	0.2386	1650	1650	48
2.5527-2.5945	0.2684	79	0.2465	1666	1666	50
2.5945-2.6392	0.2901	104	0.2421	1766	1766	51
2.6392-2.6872	0.2481	111	0.2287	1799	1799	54
2.6872-2.7389	0.283	117	0.2329	1926	1926	57
2.7389-2.7948	0.3141	106	0.2111	2131	2131	63
2.7948-2.8555	0.2465	119	0.2094	2370	2370	70
2.8555-2.9219	0.2356	136	0.2144	2724	2724	78
2.9219-2.995	0.2433	145	0.1949	2794	2794	84
2.995-3.0759	0.2471	177	0.2055	2976	2976	87
3.0759-3.1664	0.2596	144	0.2187	3061	3061	91
3.1664-3.2686	0.2333	149	0.1975	3253	3253	94
3.2686-3.3853	0.2254	151	0.1945	3306	3306	97
3.3853-3.5208	0.2167	184	0.1877	3342	3342	98
3.5208-3.6809	0.2197	188	0.1806	3308	3308	99
3.6809-3.8748	0.2122	182	0.1658	3430	3430	100
3.8748-4.1174	0.1878	178	0.1546	3363	3355	100
4.1174-4.4349	0.1759	178	0.1433	3355	3363	100
4.4349-4.8805	0.1631	174	0.1333	3416	3416	100
4.8805-5.585	0.1701	204	0.1489	3382	3382	100
5.585-7.0302	0.2043	190	0.1668	3402	3402	100
7.0302-39.7532	0.1762	170	0.1463	3352	3352	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.8214	0.8903	-0.7077	1.0629	0.1918	1.6839	-0.6764	0.7597	-0.8339	-0.483	0.3192	0.092	0.3296	-0.2524	0.2778	0.7419	-0.4792	0.4684	0.0468	-0.205	0.692	0.742	25.5488	1.7187
2	4.3561	1.9096	-0.8147	2.7358	-1.8261	1.2919	-0.3955	-0.2588	-0.2071	0.1101	-0.0212	-0.039	-0.0575	0.1288	0.3289	0.4756	0.0119	0.1349	0.1812	0.0422	0.2354	5.611	36.3943	13.0322
3	3.1013	1.9915	-2.6904	3.1133	-2.6963	3.5055	-0.3131	-0.2837	-0.4737	-0.1552	-0.1609	-0.2975	0.3123	0.4111	0.4494	0.241	-0.0121	0.0855	0.1978	0.0404	0.1918	22.7442	45.4012	4.6516
4	7.5626	0.1973	-0.4535	3.1974	-1.9269	4.2279	-0.049	-0.3684	0.2089	0.1426	0.0144	0.2331	0.0586	-0.0218	-0.018	0.1696	-0.0509	0.0669	0.1041	-0.0308	0.1875	18.6803	54.8748	3.4638
5	5.3642	1.3782	-1.1433	3.6849	-0.9765	3.2913	-0.1699	0.5277	0.3613	-0.2337	0.2763	0.3664	0.0951	-0.3347	-0.1282	0.1543	-0.1033	0.0289	0.2139	0.0795	0.14	17.1454	57.2718	-8.6375
6	1.3967	0.6948	-0.3303	1.6958	-0.0617	0.2469	-0.6979	0.7516	-0.7157	-0.5864	0.1939	-0.1014	0.854	-0.1936	0.3783	0.6471	-0.2203	0.2807	0.3838	-0.1626	0.4196	17.3933	37.7593	-11.0498
7	2.2425	0.2269	0.0504	0.7637	-0.8615	1.1326	-0.6909	0.7239	-0.8284	-0.6288	0.1541	-0.1696	0.6496	-0.1768	0.3773	0.9169	-0.127	0.6237	0.3959	-0.3083	0.7161	10.1031	23.4278	-4.0727
8	1.2365	0.7491	-0.7138	1.4117	-0.737	1.4446	-0.4887	0.2347	-0.9744	-0.3222	0.0458	-0.3665	0.4184	0.2931	0.5034	0.6145	-0.0077	0.7047	0.1024	0.3583	0.982	17.9144	24.2066	9.1995
9	2.2508	1.1848	-1.6588	1.2667	-1.2177	2.3512	-0.2771	-0.2979	-0.4804	-0.132	-0.1393	-0.3535	0.34	0.1636	0.4005	0.3419	0.0499	0.1321	0.2807	0.0731	0.3351	19.6664	40.2197	8.1431
10	2.0077	0.4921	-0.1027	0.853	-0.4846	1.2697	0.1568	-1.1842	-0.4397	0.2258	-0.5496	-0.658	-0.011	0.5114	0.2689	0.1533	0.1006	-0.002	0.8798	0.493	0.6627	76.6458	69.354	-17.6369
11	4.28	1.6125	-2.1878	1.835	-0.1178	1.5136	-0.0635	-0.0432	-0.0629	-0.3388	-0.2115	-0.1201	0.0872	-0.1804	0.2318	0.2781	0.1513	0.1277	0.3834	0.0807	0.2461	64.8482	70.6092	-28.9209
12	4.6892	0.9554	-3.5151	1.3237	-1.0513	3.4289	-0.4038	-0.0913	-0.512	-0.2421	-0.0234	-0.264	0.528	0.0308	0.4152	0.2064	-0.0002	0.0696	0.2232	0.0631	0.2035	48.509	60.2706	-20.4916
13	4.2978	1.2144	-2.2692	3.9156	-0.697	3.4377	0.04	-0.0023	0.2566	-0.0958	-0.0345	0.1035	-0.0841	0.138	-0.0227	0.0653	-0.0223	0.0289	0.2007	0.0439	0.1574	40.9575	68.9334	-15.2761
14	2.715	0.8788	-2.0988	1.9622	-0.8484	2.1647	0.2476	-0.8323	0.0525	0.3212	-0.4041	-0.1902	-0.0028	0.6272	0.2484	0.2045	-0.0752	0.0257	0.4559	0.0108	0.1771	47.5481	68.9244	-4.9203
15	1.9314	0.5312	-0.9142	0.6771	-0.409	0.5646	-0.0474	-0.9478	-0.8775	0.2684	-0.5806	-1.1881	0.4128	0.6342	0.4994	0.1859	0.1583	0.3151	0.7551	0.5156	0.667	66.623	56.9929	-13.8945
16	1.9188	0.3554	-1.0398	0.5774	0.522	1.5824	-0.495	0.4753	-0.2633	-0.4718	0.2349	-0.1487	0.4164	-0.3249	0.2338	0.4246	-0.0524	0.1431	0.3805	-0.0105	0.3354	54.9992	64.0282	-37.866

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 27 through 110 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 111 through 139 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 220 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 221 through 254 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 255 through 304 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 305 through 345 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 346 through 392 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 393 through 441 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 27 through 110 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 111 through 139 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 187 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 188 through 240 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 241 through 273 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 274 through 414 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 415 through 441 )

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